Covid 19 Exploration Project

library(tidyverse)

Registered S3 methods overwritten by 'dbplyr':
  method         from
  print.tbl_lazy     
  print.tbl_sql      
-- Attaching packages ----------------------------------------------------------------------- tidyverse 1.3.0 --
v ggplot2 3.3.5     v purrr   0.3.4
v tibble  3.1.0     v dplyr   1.0.5
v tidyr   1.1.3     v stringr 1.4.0
v readr   1.3.1     v forcats 0.5.1
-- Conflicts -------------------------------------------------------------------------- tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()

covid19 <- read_csv("data/covid19-daily-cases.csv")

Parsed with column specification:
cols(
  country_region = col_character(),
  date = col_date(format = ""),
  confirmed = col_double()
)

covid19

covid19 %>% 
  ggplot(aes(
    x = date, 
    y = confirmed, 
    colour = country_region)) +
  geom_line() +
  guides(colour = FALSE)

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

Fit with log scale so it becomes normal

covid19 %>% 
  ggplot(aes(
    x = date, 
    y = log10(confirmed),
    colour = country_region)) +
  geom_line() +
  guides(colour = FALSE)

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

covid19 %>% 
  ggplot(aes(
    x = date, 
    y = confirmed, 
    colour = country_region)) +
  geom_line() +
  guides(colour = FALSE) +
  scale_y_log10()

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: Transformation introduced infinite values in continuous y-axis

covid19_rel <- covid19 %>% 
  group_by(country_region) %>% 
  mutate(days = as.numeric(date - min(date))) %>% 
  ungroup()
covid19_rel

world <- covid19_rel %>% 
  ggplot(aes(
    x = days,
    y = confirmed, 
    colour = country_region)) +
  geom_line() +
  scale_y_log10() +
  guides(colour = FALSE)

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

world

Warning: Transformation introduced infinite values in continuous y-axis

covid19_nz <- covid19_rel %>% 
  filter(country_region == "New Zealand")
p_nz <- covid19_rel %>% 
  ggplot(aes(x = days, y = confirmed, 
    group = country_region)) +
  geom_line(colour = "grey", alpha = 0.5) +
  geom_line(colour = "#238b45", size = 1, data = covid19_nz) +
  scale_y_log10() +
  guides(colour = FALSE)

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

p_nz

Warning: Transformation introduced infinite values in continuous y-axis

p_nz <- p_nz +
  geom_label(aes(
    x = max(days), y = max(confirmed),
    label = country_region), data = covid19_nz,
    colour = "#238b45", nudge_x = 3, nudge_y = .5)
p_nz

Warning: Transformation introduced infinite values in continuous y-axis

p_nz <- p_nz +
  scale_y_log10(labels = scales::label_comma()) +
  xlim(c(0, 100))

Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale.

p_nz

Warning: Transformation introduced infinite values in continuous y-axis

p_nz <- p_nz +
  labs(
    x = "Days since March 1",
    y = "Confirmed cases (on log10)",
    title = "Worldwide coronavirus confirmed cases",
    subtitle = "highlighting New Zealand",
    caption = "Data source: John Hopkins University, CSSE"
  )
p_nz

Warning: Transformation introduced infinite values in continuous y-axis

library(plotly)

Registered S3 method overwritten by 'data.table':
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  print.data.table     
Registered S3 methods overwritten by 'htmltools':
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  print.html           tools:rstudio
  print.shiny.tag      tools:rstudio
  print.shiny.tag.list tools:rstudio
Registered S3 method overwritten by 'htmlwidgets':
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  print.htmlwidget tools:rstudio

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

ggplotly(p_nz)

Warning: Transformation introduced infinite values in continuous y-axis
Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]) :
  geom_GeomLabel() has yet to be implemented in plotly.
  If you'd like to see this geom implemented,
  Please open an issue with your example code at
  https://github.com/ropensci/plotly/issues